A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2025-04-01, 12:35 UTC
based on data in:
/home/runner/work/pmultiqc/pmultiqc/data
nf-core/quantms Software Versions
nf-core/quantms Software Versions are collected at run time from the software output.URL: https://github.com/nf-core/quantms
| Process Name | Software | Version |
|---|---|---|
| CUSTOM_DUMPSOFTWAREVERSIONS | python | 3.9.5 |
| yaml | 5.4.1 | |
| FDRIDPEP | FalseDiscoveryRate | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| IDFILTER | IDFilter | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| IDPEP | IDPosteriorErrorProbability | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| IDSCORESWITCHER | IDScoreSwitcher | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| MZMLINDEXING | FileConverter | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| PROTEOMICSLFQ | ProteomicsLFQ | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| SAMPLESHEET_CHECK | sdrf-pipelines | 0.0.21 |
| SEARCHENGINEMSGF | MSGFPlusAdapter | 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47 |
| msgf_plus | MS-GF+ Release (v2021.03.22) (22 March 2021) | |
| Workflow | Nextflow | 21.10.6 |
| nf-core/quantms | 1.1dev |
nf-core/quantms Workflow Summary
- this information is collected when the pipeline is started.URL: https://github.com/nf-core/quantms
Core Nextflow options
- runName
- hungry_linnaeus
- containerEngine
- docker
- launchDir
- /home/chengxin/newPR/quantms
- workDir
- /home/chengxin/newPR/quantms/work
- projectDir
- /home/chengxin/newPR/quantms
- userName
- chengxin
- profile
- test_lfq,docker
- configFiles
- /home/chengxin/newPR/quantms/nextflow.config
Input/output options
- input
- /home/chengxin/lfq_testdata/BSA_design_urls1.tsv
- outdir
- ./results_lfq
Protein database
- database
- /home/chengxin/lfq_testdata/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta
- decoy_string
- rev
Database search
- search_engines
- msgf
- instrument
- N/A
Modification localization
- luciphor_debug
- N/A
PSM re-scoring (general)
- posterior_probabilities
- fit_distributions
- run_fdr_cutoff
- 0.10
PSM re-scoring (Percolator)
- description_correct_features
- N/A
Consensus ID
- consensusid_considered_top_hits
- N/A
- min_consensus_support
- N/A
Isobaric analyzer
- select_activation
- HCD
Protein inference
- protein_level_fdr_cutoff
- 1.0
- psm_level_fdr_cutoff
- 1.0
Protein Quantification (DDA)
- labelling_type
- label free sample
- ratios
- N/A
- normalize
- N/A
- fix_peptides
- N/A
DIA-NN
- mass_acc_ms2
- 13
- mass_acc_ms1
- 7
- scan_window
- 8
Statistical post-processing
- contrasts
- pairwise
- add_triqler_output
- true
Quality control
- enable_pmultiqc
- true
Institutional config options
- config_profile_name
- Test profile for DDA LFQ
- config_profile_description
- Minimal test dataset to check pipeline function of the label-free quantification branch of the pipeline
Max job request options
- max_cpus
- 2
- max_memory
- 6 GB
- max_time
- 2d
Generic options
- hostnames
- N/A